Discussion

You were asked to read

• Sections 1-4 of Byran article (Excuse Me…)
• Stewart Lowndes et al (Our path…)

*What were your takeaways from the Bryan article?

*What were your takeaways from the Stewart Lowndes article?

Discussion Questions

1. What the difference between Git and Github?

Discussion Questions

1. What the difference between Git and Github?

2. In the Our path… article, the authors discuss the implementation of version control/reproducibility (via Github and RStudio) in the global OHI assessment. How do you see version control/reproducability being implemented in your research?

Discussion Questions

1. What the difference between Git and Github?

2. In the Our path… article, the authors discuss the implementation of version control/reproducibility (via Github and RStudio) in the global OHI assessment. How do you see version control/reproducability being implemented in your research?

3. What do you think will be the largest obstacle to utilizing version control with GitHub?

Happy Git and GitHub for the useR

• You all should have
  • Created your NCSU GitHub account
  • Upgraded RStudio to version 4.0
  • Installed and introduced yourself to Git (i.e completed Section 1: Installation)

To start today’s lecture

• Git is program for version control of software
  • It was not built to be user friendly!

• GitHub is the user friendly remote hosting site

• The Git extension in RStudio allows for a user friendly GUI

You can interact with Git from the Terminal/Shell

• The shell is a program that allows you to run programs on your computer
  • Similar to “terminal”, “command line”, and “console”

You can launch a shell from RStudio. This is often handy, because RStudio makes every effort to put you in a same working directory, i.e. in the current project.

• Tools > Terminal launches a shell within RStudio, graphically and process-wise.
  • This is usually what you want.

Basic Shell Commands

• pwd (print working directory).
  • Shows directory or “folder” you are currently operating in.
• ls (list files).
  • Shows the files in the current working directory. This is equivalent to looking at the files in your Finder/Explorer/File Manager.
• cd (change directory).
  • Allows you to navigate through your directories by changing the shell’s working directory. You can navigate like so:
  • go to subdirectory foo of current working directory: cd foo
  • go to parent of current working directory: cd ..
  • go to your “home” directory: simply cd
• Use arrow-up and arrow-down to repeat previous commands. Or search for previous commands with CTRL + r.

Chapter 12: Connect RStudio to Git and GitHub

Objectives:

1. Make sure that you can all pull from and push to GitHub in RStudio on your local computer
2. Use RStudio to edit, commit, and push to your remote GitHub repo

Order of operation

1. Connect to GitHub
2. Make a repository (or repo) on GitHub
3. Clone the repo to your local computer via RStudio
4. Make a local change, commit, and push
5. Confirm local change propagated to the GitHub remote
6. Clean up

Connect to GitHub

• Start by going to https://github.com and logging in

Homepage should look like this

Make a repo on GitHub

Click the plus, then the “New repository” button.

Make a repo on GitHub

Make a repo on GitHub

You should see this

Clone the repo to your local computer

Copy the HTTPS clone URL to your clipboard via the green “Clone or Download” button.

Clone the new GitHub repo to your local computer via RStudio

• All of your R projects should have this set-up.

• The new local RStudio Project should represent the new test remote repo created on GitHub

Make a local change, commit, and push

In your local RStudio Project modify the README.md file + Add the line “This is a line from RStudio” + Save your change

Now, commit these changes to your local repo. How?

In RStudio:

• Click the “Git” tab in upper right pane.
• Click the white “Staged” box for README.md.
• Click “Commit”.
• “Comment” on your “commit”!
  • “Commit message”, such as “Commit from RStudio”.
• Click “Commit”.

Pull then Push your local changes online to GitHub

• First, Pull into RStudio the most updated verison of the GitHub Repo
  • You should see some message…

Already up to date.

• Click the green “Push” button to send your local changes to GitHub. If you are challenged for username and password, provide them
  • You should see some message..

[master dc671f0] blah
 3 files changed, 22 insertions(+)
 create mode 100644 .gitignore
 create mode 100644 myrepo.Rproj

Workflow

Do work somewhere. Commit it. Push it or pull it* depending on where you did it, but get local and remote “synced up”. Repeat.

* Note that in general (and especially in future when collaborating with other developers) you will usually need to pull changes from the remote (GitHub) before pushing the local changes you have made. For this reason, it’s a good idea to try and get into the habit of pulling before you attempt to push.

Confirm local change propgated to GitHub

1. Go back to the browser. I assume we’re still viewing your new GitHub repo.

2. Refresh.

3. You should see the new “This is a line from RStudio” in the README.

4. If you click on “commits,” you should see one with the message “Commit from Rstudio”

Clean up

Local * When you’re ready to clean up, you can delete the local repo any way you like. It’s just a regular directory on your computer.

GitHub * In the browser, go to your repo’s landing page on GitHub. Click on “Settings”. * Scroll down, click on “delete repository,” and do as it asks.

Before moving on, lets discuss some of the Git methodology/terminology

• Git allows you to take snapshots of all the files in a folder

• This folder is your repository or repo

• When you commit, you take a snapshot, which you then push to Github with a comment
  • Think of taking a picture (commit) then posting (pushing) the picture to instagram
    • and you wouldn’t post a picture to instagram without a comment

Git methodology/terminology

• When you commit a file or files, additional information is saved along with the changes to the file
  • Who
  • When
  • What was changed
  • A comment on the change

Git methodology/terminology

These snapshots act as version control

Git methodology/terminology

These snapshots act as version control

Git methodology/terminology

These snapshots act as version control

Git methodology/terminology

• Git, or in our case GitHub, stores the history of your project
  • This lets you time travel to different versions of your project
  • you can check out these older versions of the project

Git methodology/terminology

• What if you want to experiment with making some changes to files in your project?
  • you can do this by creating a branch
• A branch is a moveable label attached to a commit

Git methodology/terminology

• The default branch name in GitHub is master
  • To experiment with making some changes created a new branch
  • If you are happy with the changes you can merge them back into the master
• In collaborative projects
  • most changes should be done in a new branch
  • the master branch is often the verison of the code that is published on a site

Git methodology/terminology

• As you know, it is always good to back up your work
  • Typically, not on your local computer
• This outside storage location is called a remote
  • GitHub is one very popular remote

Git methodology/terminology

• To get work from a remote for the first time you must clone it to your local computer _ We just did this!!

• If you make a change at the local level,
  1. You can commit the change
  2. Then push it back to the remote
  3. For someone else to have the most updated repo, they now need to pull your changes to their local computer

Summary

repo - your project folder

commit - snapshot of repo

checkout - time travel to specific commit

branch - a moveable label that point to a commit

merge - combining two branches

remote - a computer/server with the repository on it

clone - the first time you get the repo from the remote

push - send commits (with comments) to a remote

pull - get updated repo from a remote

• Haven’t yet discussed
• fork or pull request or upstream

Now, lets use GitHub and RStudio together (Chapter 15)

• This workflow will be similar to the previous section
• More like what you will be doing in the future by using Git within RStudio

Start by making a repo in GitHub

• This will be done using the same exact method as before
• Remember
  • Repository name: myrepo (or whatever you wish, we’ll delete this soon anyway).
  • Description: “testing my setup” (or whatever, but some text is good for the README).
  • Public.
  • YES Initialize this repository with a README.
• For everything else, just accept the default.
• Click big green button “Create repository.”

From here

• With the rest of the class period, I would like you to work on CH 15 and go through CH 16 and 17.

For Thursday (2/4/21), you need to

• Complete Chapter 15
• Finish reading Byran article (Excuse Me…)